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BMRB: 19746

2MJY

Solution structure of synthetic Mamba-1 peptide

Authors

He, Y., Wu, F., Tian, C.

Assembly

synthetic Mamba-1 peptide

Entity

1. synthetic Mamba-1 peptide (polymer), 57 monomers, 6562.545 Da Detail

LKCYQHGKVV TCHRDMKFCY HNTGMPFRNL KLILQGCSSS CSETENNKCC STDRCNK

Formula weight

6562.545 Da

Source organism

Dendroaspis polylepis

Exptl. method

Refine. method

distance geometry

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 89.5 %, Completeness: 70.7 %, Completeness (bb): 90.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	70.7 % (246 of 348)	70.7 % (246 of 348)
Backbone	90.5 % (105 of 116)	90.5 % (105 of 116)
Sidechain	60.8 % (141 of 232)	60.8 % (141 of 232)
Aromatic	16.7 % (4 of 24)	16.7 % (4 of 24)
Methyl	88.9 % (16 of 18)	88.9 % (16 of 18)

1. Mamba-1

LKCYQHGKVV TCHRDMKFCY HNTGMPFRNL KLILQGCSSS CSETENNKCC STDRCNK

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	H2O	natural abundance		90 %
3	D2O	[U-100% 2H]		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
4	sodium phosphate	natural abundance		50 mM
5	ethanol	[U-2H]		5 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
8	sodium phosphate	natural abundance		50 mM
9	TFE	[U-2H]		5 %
10	H2O	natural abundance		90 %
11	D2O	[U-100% 2H]		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2MJY, Strand ID: A Detail

Release date

2015-01-25

Citation

One-pot hydrazide-based native chemical ligation for efficient chemical synthesis and structure determination of toxin Mambalgin-1
Pan, F., He, Y., Wen, M., Wu, F., Sun, D., Liu, L., Zhang, L., Li, Y., Tian, C.
Chem. Commun. (Camb). (2014), 50, 5837-5839, PubMed 24619065 , DOI 10.1039/c4cc00779d , Abstract

Related entities 1. synthetic Mamba-1 peptide, : 1 : 6 : 2 : 2 : 95 entities Detail

Experiments performed 8 experiments Detail

1 2D DQF-COSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	H2O	natural abundance		90 %
3	D2O	[U-100% 2H]		10 %

2 2D 1H-1H TOCSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	H2O	natural abundance		90 %
3	D2O	[U-100% 2H]		10 %

3 2D 1H-1H NOESY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	H2O	natural abundance		90 %
3	D2O	[U-100% 2H]		10 %

4 2D DQF-COSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	H2O	natural abundance		90 %
3	D2O	[U-100% 2H]		10 %

5 2D 1H-1H TOCSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	H2O	natural abundance		90 %
3	D2O	[U-100% 2H]		10 %

6 2D 1H-1H NOESY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	sodium phosphate	natural abundance		50 mM
2	H2O	natural abundance		90 %
3	D2O	[U-100% 2H]		10 %

7 2D 1H-1H TOCSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
4	sodium phosphate	natural abundance		50 mM
5	ethanol	[U-2H]		5 %
6	H2O	natural abundance		90 %
7	D2O	[U-100% 2H]		10 %

8 2D 1H-1H TOCSY

Instrument

Varian INOVA - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
8	sodium phosphate	natural abundance		50 mM
9	TFE	[U-2H]		5 %
10	H2O	natural abundance		90 %
11	D2O	[U-100% 2H]		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19746_2mjy.nef
Input source #2: Coordindates	2mjy.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:3:CYS:SG	A:19:CYS:SG	unknown	unknown	2.021
A:12:CYS:SG	A:37:CYS:SG	unknown	unknown	2.02
A:41:CYS:SG	A:49:CYS:SG	unknown	unknown	2.02
A:50:CYS:SG	A:55:CYS:SG	unknown	unknown	2.023

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50-------
LKCYQHGKVVTCHRDMKFCYHNTGMPFRNLKLILQGCSSSCSETENNKCCSTDRCNK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LKCYQHGKVVTCHRDMKFCYHNTGMPFRNLKLILQGCSSSCSETENNKCCSTDRCNK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	57	0	0	100.0

Content subtype: combined_19746_2mjy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	236		87.7 (chain: A, length: 57)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	814 (1)	noe	89.5 (chain: A, length: 57)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 87.7%
- Total number of assignments
  - ¹H chemical shifts: 236
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 57, Sequence coverage: 89.5%
- Total number of restraints: 814
- Weight of restraints: 1.0 (814)
- Potential type of restraints: square-well-parabolic (814)
- Range of distance target values: 2.4, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Manba, toxin